IncompressibleElasticVarForm.cpp

Go to the documentation of this file.

#include "IncompressibleElasticVarForm.hpp"
 
#include <cmath>
#include <numeric>
#include <algorithm>
 
#include <polyfem/assembler/AssemblerUtils.hpp>
#include <polyfem/basis/LagrangeBasis2d.hpp>
#include <polyfem/basis/LagrangeBasis3d.hpp>
#include <polyfem/mesh/mesh2D/Mesh2D.hpp>
#include <polyfem/mesh/mesh3D/Mesh3D.hpp>
#include <polyfem/time_integrator/BDF.hpp>
#include <polyfem/utils/Logger.hpp>
#include <polyfem/utils/MatrixUtils.hpp>
#include <polyfem/utils/Timer.hpp>
#include <polyfem/varforms/VarFormUtils.hpp>
 
#include <polysolve/linear/FEMSolver.hpp>
 
namespace polyfem::varform
{
    using namespace varform::internal;
 
    void IncompressibleElasticVarForm::serialize_checkpoint(
        io::CheckpointWriter &writer,
        const Eigen::MatrixXd &solution,
        const io::CheckpointMetadata &metadata) const
    {
        VarForm::serialize_checkpoint(writer, solution, metadata);
        write_checkpoint_ordering(writer, "primary", space_);
        write_checkpoint_ordering(writer, "pressure", pressure_space_);
    }
 
    void IncompressibleElasticVarForm::deserialize_checkpoint(
        const io::CheckpointReader &reader,
        Eigen::MatrixXd &solution)
    {
        VarForm::deserialize_checkpoint(reader, solution);
        validate_checkpoint_solution(solution, stacked_ndof());
        reorder_checkpoint_block(
            reader, "primary", space_,
            mesh_->dimension(), 0, solution);
        reorder_checkpoint_block(
            reader, "pressure", pressure_space_,
            1, primary_ndof(), solution);
    }
 
    void IncompressibleElasticVarForm::reset()
    {
        ElasticVarForm::reset();
        pressure_space_.reset();
        displacement_space_id_ = -1;
        pressure_space_id_ = -1;
        pressure_boundary_.reset();
        pressure_ass_vals_cache_.init_empty();
        mixed_assembler_ = nullptr;
        pressure_assembler_ = nullptr;
        time_integrator = nullptr;
    }
 
    void IncompressibleElasticVarForm::init(const std::string &formulation, const Units &units, const json &args, const std::string &out_path)
    {
        ElasticVarForm::init(formulation, units, args, out_path);
        const json &discr_orders = args.at("space").at("discr_order");
 
        const json &materials = args.at("materials");
        if (materials.is_array() && materials.empty())
            log_and_throw_error("Incompressible elasticity requires at least one material.");
        const json &first_material = materials.is_array() ? materials.at(0) : materials;
        displacement_space_id_ = first_material.at("displacement_space_id").get<int>();
        pressure_space_id_ = first_material.at("pressure_space_id").get<int>();
        if (displacement_space_id_ == pressure_space_id_)
            log_and_throw_error("Incompressible displacement and pressure must use different FE space IDs.");
 
        if (discr_orders.is_array())
        {
            bool has_displacement_space = false;
            bool has_pressure_space = false;
            for (const json &entry : discr_orders)
            {
                const int fe_space_id = entry.at("fe_space").get<int>();
                has_displacement_space |= fe_space_id == displacement_space_id_;
                has_pressure_space |= fe_space_id == pressure_space_id_;
            }
            if (!has_displacement_space || !has_pressure_space)
                log_and_throw_error("Incompressible discretization-order lists must explicitly name the displacement and pressure FE spaces.");
        }
 
        if (materials.is_array())
        {
            for (const json &material : materials)
            {
                if (material.at("displacement_space_id").get<int>() != displacement_space_id_
                    || material.at("pressure_space_id").get<int>() != pressure_space_id_)
                    log_and_throw_error("All incompressible materials must use the same displacement and pressure FE space IDs.");
            }
        }
 
        mixed_assembler_ = assembler::AssemblerUtils::make_mixed_assembler(formulation);
        pressure_assembler_ = assembler::AssemblerUtils::make_assembler(assembler::AssemblerUtils::other_assembler_name(formulation));
        assert(primary_assembler_->is_linear());
        assert(primary_assembler_->is_tensor());
    }
 
    void IncompressibleElasticVarForm::save_json(const Eigen::MatrixXd &solution, std::ostream &out) const
    {
        if (!mesh_)
        {
            logger().error("Load the mesh first!");
            return;
        }
        if (solution.size() <= 0)
        {
            logger().error("Solve the problem first!");
            return;
        }
 
        logger().info("Saving json...");
        const int primary_size = primary_ndof();
        const Eigen::MatrixXd stats_solution =
            solution.rows() >= primary_size
                ? solution.topRows(primary_size).eval()
                : solution;
 
        nlohmann::json j;
        stats.save_json(
            args, space_.n_bases, pressure_space_.n_bases,
            stats_solution, *mesh_, space_.disc_orders, space_.disc_ordersq, *problem,
            timings, primary_assembler_ ? primary_assembler_->name() : name(), space_.is_iso_parametric(),
            args["output"]["advanced"]["sol_at_node"], j);
        out << j.dump(4) << std::endl;
    }
 
    io::OutStatsData IncompressibleElasticVarForm::compute_errors(const Eigen::MatrixXd &solution)
    {
        if (!args["output"]["advanced"]["compute_error"])
            return stats;
 
        double tend = 0;
        if (!args["time"].is_null())
            tend = args["time"]["tend"];
 
        Eigen::MatrixXd displacement, pressure;
        split_solution(solution, displacement, pressure);
        stats.compute_errors(space_.n_bases, space_.basis_list(), space_.geometry_basis_list(), *mesh_, *problem, tend, displacement);
        return stats;
    }
 
    void IncompressibleElasticVarForm::load_mesh(const mesh::Mesh &mesh, const json &args)
    {
        ElasticVarForm::load_mesh(mesh, args);
        if (mixed_assembler_)
            mixed_assembler_->set_size(mesh.dimension());
        if (pressure_assembler_)
            set_materials(*pressure_assembler_, mesh.dimension());
    }
 
    int IncompressibleElasticVarForm::primary_ndof() const
    {
        return mesh_ ? space_.n_bases * mesh_->dimension() : 0;
    }
 
    int IncompressibleElasticVarForm::stacked_ndof() const
    {
        return primary_ndof() + pressure_space_.n_bases;
    }
 
    void IncompressibleElasticVarForm::build_rhs_assembler()
    {
        json rhs_solver_params = args["solver"]["linear"];
        if (!rhs_solver_params.contains("Pardiso"))
            rhs_solver_params["Pardiso"] = {};
        rhs_solver_params["Pardiso"]["mtype"] = -2;
 
        rhs_assembler_ = std::make_shared<assembler::RhsAssembler>(
            *primary_assembler_, *mesh_, nullptr,
            boundary_.dirichlet_nodes, boundary_.neumann_nodes,
            boundary_.dirichlet_nodes_position, boundary_.neumann_nodes_position,
            space_.n_bases, mesh_->dimension(), space_.basis_list(), space_.geometry_basis_list(), mass_ass_vals_cache_, *problem, resources_,
            args["space"]["advanced"]["bc_method"],
            rhs_solver_params,
            displacement_space_id_);
    }
 
    void IncompressibleElasticVarForm::build_basis(mesh::Mesh &mesh, const bool iso_parametric, const json &args)
    {
        build_elastic_basis(mesh, iso_parametric, args, displacement_space_id_);
 
        if (space_.disc_orders.maxCoeff() != space_.disc_orders.minCoeff())
            log_and_throw_error("p refinement not supported in mixed formulation!");
        if (!space_.poly_edge_to_data.empty())
            log_and_throw_error("Polygonal bases are not supported in mixed formulations!");
 
        const auto &all_boundary = boundary_.total_local_boundary;
        const int prev_bases = space_.n_bases;
        const bool use_corner_quadrature = args["space"]["advanced"]["use_corner_quadrature"];
        const int quadrature_order = args["space"]["advanced"]["quadrature_order"].get<int>();
        const int mass_quadrature_order = args["space"]["advanced"]["mass_quadrature_order"].get<int>();
        Eigen::VectorXi pressure_disc_orders, pressure_disc_ordersq;
        assign_discr_orders(args["space"], pressure_space_id_, mesh, pressure_disc_orders, pressure_disc_ordersq);
        // to avoid serendipity
        const std::string pressure_basis_type = args["space"]["basis_type"].get<std::string>() == "Bernstein" ? "Bernstein" : "Lagrange";
        build_fe_space(
            mesh,
            /*iso_parametric=*/true,
            pressure_disc_orders,
            pressure_disc_ordersq,
            pressure_basis_type,
            args["space"]["poly_basis_type"],
            *primary_assembler_,
            /*value_dim=*/1,
            quadrature_order,
            mass_quadrature_order,
            use_corner_quadrature,
            args["space"]["advanced"]["n_harmonic_samples"],
            args["space"]["advanced"]["integral_constraints"],
            pressure_space_,
            pressure_boundary_,
            space_.geometry);
 
        assert(space_.basis_list().size() == pressure_space_.basis_list().size());
        for (int i = 0; i < int(pressure_space_.basis_list().size()); ++i)
        {
            quadrature::Quadrature b_quad;
            space_.basis_list()[i].compute_quadrature(b_quad);
            (*pressure_space_.bases)[i].set_quadrature([b_quad](quadrature::Quadrature &quad) { quad = b_quad; });
        }
 
        boundary_.clear_boundary_conditions();
        for (const auto &lb : all_boundary)
            boundary_.local_boundary.emplace_back(lb);
        pressure_boundary_.clear_boundary_conditions();
 
        problem->setup_bc(
            mesh, space_.n_bases,
            space_.basis_list(), space_.geometry_basis_list(), pressure_space_.basis_list(),
            boundary_.local_boundary,
            boundary_.boundary_nodes,
            boundary_.local_neumann_boundary,
            boundary_.local_pressure_boundary,
            boundary_.local_pressure_cavity,
            pressure_boundary_.boundary_nodes,
            boundary_.dirichlet_nodes, boundary_.neumann_nodes);
        pressure_boundary_.normalize_boundary_nodes();
 
        rebuild_node_positions(space_.basis_list(), boundary_.dirichlet_nodes, boundary_.dirichlet_nodes_position);
        rebuild_node_positions(space_.basis_list(), boundary_.neumann_nodes, boundary_.neumann_nodes_position);
 
        for (int i = prev_bases; i < space_.n_bases; ++i)
            for (int d = 0; d < mesh.dimension(); ++d)
                boundary_.boundary_nodes.push_back(i * mesh.dimension() + d);
 
        boundary_.normalize_boundary_nodes();
 
        if (space_.n_bases <= args["solver"]["advanced"]["cache_size"])
            pressure_ass_vals_cache_.init(mesh.is_volume(), pressure_space_.basis_list(), space_.geometry_basis_list());
        else
            pressure_ass_vals_cache_.init_empty();
 
        build_rhs_assembler();
 
        logger().info("n pressure bases: {}", pressure_space_.n_bases);
    }
 
    void IncompressibleElasticVarForm::assemble_rhs(const mesh::Mesh &mesh)
    {
        ElasticVarForm::assemble_rhs(mesh);
        const int prev_size = rhs_.rows();
        rhs_.conservativeResize(prev_size + pressure_space_.n_bases, rhs_.cols());
        rhs_.bottomRows(pressure_space_.n_bases).setZero();
    }
 
    void IncompressibleElasticVarForm::assemble_mass_mat(const mesh::Mesh &mesh, const json &args)
    {
        if (!problem->is_time_dependent())
        {
            avg_mass_ = 1;
            timings.assembling_mass_mat_time = 0;
            return;
        }
 
        mass_.resize(0, 0);
        igl::Timer timer;
        timer.start();
        logger().info("Assembling mass mat...");
        mass_assembler_->assemble(mesh.is_volume(), space_.n_bases, space_.basis_list(), space_.geometry_basis_list(), mass_ass_vals_cache_, 0, mass_, true);
        avg_mass_ = 0;
        for (int k = 0; k < mass_.outerSize(); ++k)
            for (StiffnessMatrix::InnerIterator it(mass_, k); it; ++it)
            {
                assert(it.col() == k);
                avg_mass_ += it.value();
            }
        avg_mass_ /= std::max(1, int(mass_.rows()));
        if (args["solver"]["advanced"]["lump_mass_matrix"])
            mass_ = utils::lump_matrix(mass_);
        timer.stop();
        timings.assembling_mass_mat_time = timer.getElapsedTime();
        logger().info(" took {}s", timings.assembling_mass_mat_time);
        stats.nn_zero = mass_.nonZeros();
        stats.num_dofs = mass_.rows();
        stats.mat_size = (long long)mass_.rows() * (long long)mass_.cols();
    }
 
    void IncompressibleElasticVarForm::prepare_initial_solution(Eigen::MatrixXd &sol) const
    {
        if (sol.size() <= 0)
            initial_solution(sol);
        if (sol.cols() > 1)
            sol.conservativeResize(Eigen::NoChange, 1);
        sol.conservativeResize(stacked_ndof(), sol.cols());
        sol.bottomRows(pressure_space_.n_bases).setZero();
    }
 
    void IncompressibleElasticVarForm::split_solution(const Eigen::MatrixXd &stacked, Eigen::MatrixXd &primary, Eigen::MatrixXd &pressure) const
    {
        const int cols = std::max(1, int(stacked.cols()));
        primary.setZero(primary_ndof(), cols);
        pressure.setZero(pressure_space_.n_bases, cols);
        const int primary_rows = std::min(primary_ndof(), int(stacked.rows()));
        if (primary_rows > 0)
            primary.topRows(primary_rows) = stacked.topRows(primary_rows);
        if (stacked.rows() > primary_ndof())
        {
            const int pressure_rows = std::min(pressure_space_.n_bases, int(stacked.rows()) - primary_ndof());
            if (pressure_rows > 0)
                pressure.topRows(pressure_rows) = stacked.middleRows(primary_ndof(), pressure_rows);
        }
    }
 
    void IncompressibleElasticVarForm::build_stiffness_mat(StiffnessMatrix &stiffness)
    {
        igl::Timer timer;
        timer.start();
        logger().info("Assembling stiffness mat...");
 
        StiffnessMatrix elastic_stiffness, mixed_stiffness, pressure_stiffness;
        primary_assembler_->assemble(mesh_->is_volume(), space_.n_bases, space_.basis_list(), space_.geometry_basis_list(), ass_vals_cache_, 0, elastic_stiffness);
        mixed_assembler_->assemble(mesh_->is_volume(), pressure_space_.n_bases, space_.n_bases, pressure_space_.basis_list(), space_.basis_list(), space_.geometry_basis_list(), pressure_ass_vals_cache_, ass_vals_cache_, 0, mixed_stiffness);
        pressure_assembler_->assemble(mesh_->is_volume(), pressure_space_.n_bases, pressure_space_.basis_list(), space_.geometry_basis_list(), pressure_ass_vals_cache_, 0, pressure_stiffness);
 
        assembler::AssemblerUtils::merge_mixed_matrices(
            space_.n_bases, pressure_space_.n_bases, mesh_->dimension(), /*add_average=*/false,
            elastic_stiffness, mixed_stiffness, pressure_stiffness, stiffness);
 
        timer.stop();
        timings.assembling_stiffness_mat_time = timer.getElapsedTime();
        logger().info(" took {}s", timings.assembling_stiffness_mat_time);
        stats.nn_zero = stiffness.nonZeros();
        stats.num_dofs = stiffness.rows();
        stats.mat_size = (long long)stiffness.rows() * (long long)stiffness.cols();
        write_matrix_market(args, stiffness);
    }
 
    void IncompressibleElasticVarForm::solve_linear_system(
        const std::unique_ptr<polysolve::linear::Solver> &solver,
        StiffnessMatrix &A,
        Eigen::VectorXd &b,
        const bool compute_spectrum,
        Eigen::MatrixXd &sol)
    {
        Eigen::VectorXd x;
        stats.spectrum = dirichlet_solve(
            *solver,
            A,
            b,
            boundary_.boundary_nodes,
            x,
            primary_ndof(),
            args["output"]["data"]["stiffness_mat"],
            compute_spectrum,
            /*is_fluid=*/false,
            /*use_avg_pressure=*/false);
        sol = x;
        solver->get_info(stats.solver_info);
    }
 
    void IncompressibleElasticVarForm::solve_static_linear(Eigen::MatrixXd &sol)
    {
        auto solver = polysolve::linear::Solver::create(args["solver"]["linear"], logger());
        logger().info("{}...", solver->name());
        rhs_assembler_->set_bc(boundary_.local_boundary, boundary_.boundary_nodes, elastic_boundary_samples(), boundary_.local_neumann_boundary, rhs_);
        StiffnessMatrix A;
        build_stiffness_mat(A);
        Eigen::VectorXd b = rhs_;
        solve_linear_system(solver, A, b, args["output"]["advanced"]["spectrum"], sol);
    }
 
    void IncompressibleElasticVarForm::solve_transient_linear(Eigen::MatrixXd &sol)
    {
        auto solver = polysolve::linear::Solver::create(args["solver"]["linear"], logger());
        logger().info("{}...", solver->name());
 
        Eigen::MatrixXd displacement, pressure;
        split_solution(sol, displacement, pressure);
        auto bdf = time_integrator::ImplicitTimeIntegrator::construct_bdf_integrator(
            args["time"]["integrator"]);
        bdf->init(
            displacement,
            Eigen::MatrixXd::Zero(displacement.rows(), displacement.cols()),
            Eigen::MatrixXd::Zero(displacement.rows(), displacement.cols()),
            dt);
        time_integrator = bdf;
        restore_checkpoint_integrator(
            time_integrator, "/checkpoint/state/primary_integrator", dt,
            "primary", space_, mesh_->dimension());
 
        save_timestep(t0, 0, t0, dt, sol);
 
        Eigen::MatrixXd current_rhs = rhs_;
        StiffnessMatrix stiffness, expanded_mass;
        build_stiffness_mat(stiffness);
        expand_primary_matrix(stacked_ndof(), mass_, expanded_mass);
 
        for (int t = 1; t <= time_steps; ++t)
        {
            const double time = t0 + t * dt;
            rhs_assembler_->compute_energy_grad(
                boundary_.local_boundary, boundary_.boundary_nodes, mass_assembler_->density(), elastic_boundary_samples(), boundary_.local_neumann_boundary, rhs_, time,
                current_rhs);
            rhs_assembler_->set_bc(
                boundary_.local_boundary, boundary_.boundary_nodes, elastic_boundary_samples(), boundary_.local_neumann_boundary, current_rhs, displacement, time);
 
            if (current_rhs.rows() != stacked_ndof())
            {
                const int old_rows = current_rhs.rows();
                current_rhs.conservativeResize(stacked_ndof(), current_rhs.cols());
                if (stacked_ndof() > old_rows)
                    current_rhs.bottomRows(stacked_ndof() - old_rows).setZero();
            }
            current_rhs.bottomRows(pressure_space_.n_bases).setZero();
 
            StiffnessMatrix A = expanded_mass / bdf->beta_dt() + stiffness;
            Eigen::VectorXd b = Eigen::VectorXd::Zero(stacked_ndof());
            b.head(primary_ndof()) = (mass_ * bdf->weighted_sum_x_prevs()) / bdf->beta_dt();
            for (int i : boundary_.boundary_nodes)
                b[i] = 0;
            b += current_rhs;
 
            solve_linear_system(solver, A, b, args["output"]["advanced"]["spectrum"].get<bool>() && t == time_steps, sol);
            split_solution(sol, displacement, pressure);
            bdf->update_quantities(displacement.col(0));
 
            save_timestep(time, t, t0, dt, sol);
            save_elastic_step_state(t0, dt, t, sol, time_integrator.get());
            logger().info("{}/{}  t={}", t, time_steps, time);
            notify_time_step(t, time_steps, t0, dt);
        }
    }
 
    void IncompressibleElasticVarForm::solve_problem(
        Eigen::MatrixXd &sol,
        const InitialConditionOverride *initial_condition_override,
        const ForwardStepCallback &post_step)
    {
        assert(!initial_condition_override && "Incompressible elasticity does not support initial-condition overrides");
        assert(!post_step && "Incompressible elasticity does not support post-step callbacks");
 
        stats.spectrum.setZero();
        igl::Timer timer;
        timer.start();
        logger().info("Solving {}", primary_assembler_->name());
        prepare_initial_solution(sol);
        if (problem->is_time_dependent())
            solve_transient_linear(sol);
        else
        {
            time_integrator = nullptr;
            solve_static_linear(sol);
        }
        timer.stop();
        timings.solving_time = timer.getElapsedTime();
        logger().info(" took {}s", timings.solving_time);
    }
 
    std::vector<io::OutputField> IncompressibleElasticVarForm::output_fields(
        const io::OutputSample &sample,
        const Eigen::MatrixXd &solution,
        const io::OutputFieldOptions &options) const
    {
        Eigen::MatrixXd displacement, pressure;
        split_solution(solution, displacement, pressure);
        const std::vector<std::pair<std::string, std::shared_ptr<solver::Form>>> named_forms;
        auto fields = elastic_output_fields(
            sample, displacement, options, nullptr, time_integrator.get(), named_forms, nullptr);
        const bool export_pressure_gradient =
            !options.fields.empty() && options.export_field("pressure_gradient");
        if (mesh_ && (options.export_field("pressure") || export_pressure_gradient))
        {
            Eigen::MatrixXd values, gradients;
            if (sample_scalar_field(
                    *mesh_, pressure_space_.basis_list(), space_.geometry_basis_list(), sample, pressure, values,
                    export_pressure_gradient ? &gradients : nullptr))
            {
                if (options.export_field("pressure"))
                    fields.push_back({"pressure", values, io::OutputField::Association::Point});
                if (export_pressure_gradient)
                    fields.push_back({"pressure_gradient", gradients, io::OutputField::Association::Point});
            }
        }
        return fields;
    }
} // namespace polyfem::varform